Mercurial > repos > ppericard > viscorvar

annotate mixomics_blocksplsda.xml @ 3:df8428358b7f draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
author ppericard
date Fri, 23 Oct 2020 11:26:18 +0000
parents c8533e9298e5
children d4e9f7546dfa
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1 <tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
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3 <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description>
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5 <macros>
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6 <import>macros.xml</import>
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7 <import>macros_mixomics.xml</import>
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8 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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13 <command detect_errors="aggressive"><![CDATA[
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0
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15 mkdir outdir
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16 && @COMMAND_RSCRIPT@/mixomics_blocksplsda.R
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0
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18 #for $b in $blocks
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19 --block
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20 #if $b.block_name
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21 ${b.block_name}
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22 #else
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23 ${b.data_matrix.name}
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24 #end if
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25 ${b.keep}
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26 ${b.data_matrix}
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27 ${b.variable_metadata}
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28 #end for
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30 --sample_metadata_in ${sample_metadata_in}
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31 --sample_description_col ${sample_description_col}
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33 --ncomp ${adv.ncomp}
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34 ${correlation}
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35 ##--scheme ${adv.scheme}
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36 ##--mode ${adv.mode}
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37 --maxiter ${adv.maxiter}
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38 ##${adv.scale}
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39 --scale ## always activated hidden param
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40 ${adv.check_missing_values}
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41 ##--init ${adv.init}
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42 ##--tol ${adv.tol}
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43 ##${adv.nearzerovar}
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44
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45 --rdata_out ${rdata_out}
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46 ##--sample_metadata_out ${sample_metadata_out}
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47 --variable_metadata_outdir outdir
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48
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49 @COMMAND_LOG_EXIT@
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50
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51 ]]></command>
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52
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53 <inputs>
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54 <repeat name="blocks" title="Blocks">
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55 <param name="block_name" type="text" label="Block name" />
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56 <param name="keep" type="integer" value="0" min="0"
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57 label="Number of variables to select for each component"
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58 help="[keep] Estimation of the number of variables in the block correlated with variables from the other blocks and correlated with response variables. If set to 0, all variables will be selected." />
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59 <param name="data_matrix" type="data" format="tabular"
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60 label="Data matrix"
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61 help="Block data in tabular format (rows = variables, columns = samples). The first column contains the variables names and the first row contains the samples names. Samples names must be in the same order for all blocks and the sample metadata (transposed). The data must not contain missing values." />
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62 <param name="variable_metadata" type="data" format="tabular" optional="true"
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63 label="Variables metadata [optional]"
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64 help="Variables metadata in tabular format (rows = variables). The first colum contains the variables names. The first row contains the metadata column names. The number of rows in the metadata file must be the same than the number of rows in the block data file, and the variables need to be in the same order. If a metadata file is provided, block.splsda output will be appended as new columns, otherwise a new file will be created." />
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65 </repeat>
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66 <param name="sample_metadata_in" type="data" format="tabular"
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67 label="Samples metadata"
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68 help="Samples metadata in tabular format (rows = samples). The first column contains the sample names. The first row contains the metadata column names. Samples names must be in the same order (transposed) than all the blocks. One of the column (the last by default) must contain the samples groups for integration." />
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69 <param name="sample_description_col" type="integer" value="0" min="0"
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70 label="Samples groups column number"
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71 help="Column from the samples metadata file containing samples groups. If set to 0, the last column will be used." />
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72 <param name="correlation" type="boolean" truevalue="--correlation"
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73 falsevalue="" checked="false"
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74 label="Correlation between all blocks"
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75 help="[design] If set to Yes, data integration will take into account correlations between all the blocks (design matrix with diagonal coefficients set to 0 and the rest of the coefficients set to 1)." />
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76 <section name="adv" title="Advanced Options" expanded="false">
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77 <param name="ncomp" type="integer" value="2" min="1"
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78 label="Number of components to include in the model"
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79 help="[ncomp] Number of new variables (components) computed by the data integration." />
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80 <!-- <param name="scheme" type="select" label="Scheme">
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81 <option value="horst" selected="true">horst</option>
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82 <option value="factorial" >factorial</option>
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83 <option value="centroid" >centroid</option>
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84 </param>
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85 <param name="mode" type="select" label="Mode">
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86 <option value="regression" selected="true">regression</option>
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87 <option value="canonical" >canonical</option>
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88 <option value="invariant" >invariant</option>
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89 <option value="classic" >classic</option>
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90 </param> -->
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91 <param name="maxiter" type="integer" value="100" min="1"
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92 label="Maximum number of iterations"
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93 help="[max.iter] Maximum number of iterations performed by block.splsda." />
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94 <!-- <param name="scale" type="boolean" truevalue="-\-scale" falsevalue="" checked="true"
0
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95 label="Scale"
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96 help="if checked, each block is standardized to zero means and unit variances" /> -->
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97 <param name="check_missing_values" type="boolean" truevalue="-\-check_missing_values" falsevalue="" checked="true"
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98 label="Check for missing values"
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99 help="will raise an error if missing values are found in data matrices" />
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100 <!-- <param name="init" type="select" label="Init">
0
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101 <option value="svd" selected="true">svd</option>
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102 <option value="svd.single" >svd.single</option>
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103 </param>
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104 <param name="tol" type="float" value="1e-06" min="0"
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105 label="Convergence stopping value"
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106 help="[tol]" />
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107 <param name="nearzerovar" type="boolean" truevalue="-\-nearzerovar" falsevalue="" checked="true"
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108 label="Should be set to TRUE in particular for data with many zero values" /> -->
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109 </section>
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110 </inputs>
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111
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112 <outputs>
2
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113 <data name="rdata_out" format="rdata" label="${tool.name}_output.RData" />
1
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114 <!-- <data name="sample_metadata_out" format="tabular"
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115 label="${tool.name}_${sample_metadata_in.name}" /> -->
0
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116 <collection name="blocks_output" type="list" label="${tool.name}_blocks_output">
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117 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv"
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118 directory="outdir" format="tabular" />
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119 </collection>
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120 </outputs>
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121
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122 <tests>
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123 <test>
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124 <repeat name="blocks">
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125 <param name="block_name" value="Block1" />
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126 <param name="data_matrix" value="in_block1_data.tabular" />
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127 </repeat>
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128 <repeat name="blocks">
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129 <param name="block_name" value="Block2" />
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130 <param name="data_matrix" value="in_block2_data.tabular" />
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131 </repeat>
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132 <param name="sample_metadata_in" value="in_sample_meta.tabular" />
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133 <output name="rdata_out" value="out_rdata.rdata" />
2
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134 <!-- <output name="sample_metadata_out" value="out_sample_meta.tabular" /> -->
0
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135 </test>
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136 </tests>
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137
2
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138 <help><![CDATA[
0
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139
2
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140 @HELP_AUTHORS@
0
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141
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142 ======================
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143 mixOmics blocks.splsda
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144 ======================
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145
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146 -----------
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147 Description
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148 -----------
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149
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150 The blocks.splsda function is part of the mixOmics package for exploration and integration of Omics datasets.
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151 Performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis.
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152
2
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153 -----------------
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154 Workflow position
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155 -----------------
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156
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157 **Downstream tools**
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158
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159 ======================= ================================== ==========
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160 Name Output file Format
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161 ======================= ================================== ==========
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162 mixOmics.plotIndiv mixomics_blocksplsda_output.RData rdata
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163 ----------------------- ---------------------------------- ----------
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164 mixOmics.plotVar mixomics_blocksplsda_output.RData rdata
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165 ----------------------- ---------------------------------- ----------
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166 visCorVar.matCorAddVar mixomics_blocksplsda_output.RData rdata
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167 ======================= ================================== ==========
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168
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169 ---------------------------------------------------
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170
0
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171 -----------
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172 Input files
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173 -----------
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174
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175 For each block (min 2 blocks):
2
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176 ------------------------------
0
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177
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178 +------------------------------+------------+
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179 | Parameter : num + label | Format |
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180 +==============================+============+
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181 | 1 : Data matrix | tabular |
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182 +------------------------------+------------+
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183 | 2 : [opt] Variables metadata | tabular |
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184 +------------------------------+------------+
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185
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186 Variables metadata files are optional.
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187 If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created.
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188
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189 1. Data matrix format
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190 * Rows = variables, Columns = samples
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191 * First row = samples name. MUST be the same and in the same order in every block as well as in the sample metadata file (transposed)
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192 * First column = variables name
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193
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194 2. Variables metadata format
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195 * Rows = variables, Columns = metadata
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196 * First row = metadata column names
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197 * First column = variables names. MUST be the same and in the same order than in the associated data matrix
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198
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199 Global input files:
2
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200 -------------------
0
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201
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202 +-----------------------------+------------+
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203 | Parameter : num + label | Format |
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204 +=============================+============+
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205 | 1 : Samples metadata | tabular |
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206 +-----------------------------+------------+
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207
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208 By default, the last column of the samples metadata matrix will be used as samples description factors.
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209 If it's not the case, the column number can be inputed in the `Sample description column number` parameter.
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210
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211 1. Samples metadata format
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212 * Rows = samples, Columns = metadata
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213 * First row = metadata column names
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214 * First column = sample names. These names must be identical (transposed) and in the same order than for the blocks data matrices
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215
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216 ----------
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217 Parameters
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218 ----------
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219
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220 For each block (min 2 blocks):
2
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221 ------------------------------
0
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222
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223 Block name
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224 Name of the block. If not provided, this will default to the input filename
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225
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226 Number of variables to select for each component
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227 If set to 0 (default), all variables will be considered in the model
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228
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229 Global parameters:
2
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230 ------------------
0
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231
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232 Sample description column number
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233
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234 Number of components to include in the model
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235
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236 Correlation between all blocks
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237
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238 Advanced options:
2
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239 -----------------
0
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240
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241 Scheme
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242
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243 Mode
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244
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245 Maximum number of iterations
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246
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247 Scale
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248
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249 Init
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250
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251 Convergence stopping value (tol)
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252
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253 Near zero var
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254
2
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255
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256 @HELP_MANUAL@
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257
0
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258 ------------
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259 Output files
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260 ------------
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261
2
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262 mixomics_blocksplsda_output.RData
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263 | RData output
0
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264 | Contains the `mixomics_result` R object containing the result of the block.splsda function
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265
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266 mixomics_blocksplsda_blocks_output
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267 A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block
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268
2
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269 ]]></help>
0
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270
2
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271 <expand macro="citations" />
0
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272
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ppericard
parents:
diff changeset
273 </tool>